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- PDB-6yje: Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inh... -

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Basic information

Entry
Database: PDB / ID: 6yje
TitlePlasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from PEG3350 and ammonium acetate at pH 5.5
ComponentsPhosphoglycerate kinase
KeywordsBIOSYNTHETIC PROTEIN / phosphoglycerate kinase / metabolic enzyme / kinase
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding
Similarity search - Function
Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature.
Similarity search - Domain/homology
Chem-OTQ / Phosphoglycerate kinase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsBlaszczyk, B.K. / Hyvonen, M.
CitationJournal: to be published
Title: Phosphoglycerate Kinase as a potential target for antimalarial therapy
Authors: Bilsland, E. / Costa, F. / Blaszczyk, B.K. / Hyvonen, M. / Sunnerhagen, P.
History
DepositionApr 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 2.0May 11, 2022Group: Database references / Non-polymer description / Structure summary
Category: chem_comp / database_2 / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight
Revision 2.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5182
Polymers45,1991
Non-polymers3191
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18640 Å2
Unit cell
Length a, b, c (Å)41.962, 81.246, 124.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoglycerate kinase


Mass: 45199.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_070025900, PVP01_0721000, PVT01_070026100 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1G4HAR7, phosphoglycerate kinase
#2: Chemical ChemComp-OTQ / (2~{S})-2-(5-nitrofuran-2-yl)-2,3,5,6,7,8-hexahydro-1~{H}-[1]benzothiolo[2,3-d]pyrimidin-4-one


Mass: 319.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.49 % / Mosaicity: 0.1 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M NH4 Acet, 25 % w/v PEG 3350, 0.1 M BIS-TRIS 5.5 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→68.01 Å / Num. obs: 54681 / % possible obs: 99.9 % / Redundancy: 20.1 % / Biso Wilson estimate: 33.06 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.02 / Rrim(I) all: 0.094 / Net I/σ(I): 16.9 / Num. measured all: 1099791
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.62-1.7111.92.5649280977850.4590.7532.6780.899.6
5.13-68.0119.10.03836958193010.0090.03959.6100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y3A

6y3a


Resolution: 1.62→23.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.097
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2626 4.85 %RANDOM
Rwork0.196 ---
obs0.198 54181 98.6 %-
Displacement parametersBiso max: 97.37 Å2 / Biso mean: 35.66 Å2 / Biso min: 19.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.052 Å20 Å20 Å2
2---5.6344 Å20 Å2
3---5.5823 Å2
Refinement stepCycle: final / Resolution: 1.62→23.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 22 320 3510
Biso mean--47.23 45.63 -
Num. residues----416
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1220SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes485HARMONIC5
X-RAY DIFFRACTIONt_it3298HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion436SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4068SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3298HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4448HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion17.36
LS refinement shellResolution: 1.62→1.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3075 143 4.35 %
Rwork0.268 3144 -
all0.2698 3287 -
obs--82.14 %

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